Study of evolutionary mechanism based on comparative genome analysis

2009 Fiscal Year Final Research Report

• Project/Area Number: 17018032
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: National Institute of Genetics
• Principal Investigator: SAITOU Naruya National Institute of Genetics, 集団遺伝研究系, 教授 (30192587)
• Co-Investigator(Kenkyū-buntansha): SATTA Yoko 総合研究大学院大学, 先導科学研究科, 教授 (20222010)
• Project Period (FY): 2005 – 2009
• Keywords: 遺伝学 / 遺伝子 / ゲノム / 進化 / 人類学

Research Abstract

We obtained series of results shown as follows : discovery of gene conversion with high frequency on tandem duplicate genes of mammalian genomes ; development of rapid multiple alignment system MISHIMA for large scale nucleotide sequences ; discovery of intragenic recombination occurred million years ago through phylogenetic network analysis ; discovery of high rate of reconstruction of closely related bacterial phylogeny based on frequency pattern of oligonucleotides ; molecular evolutionary analyses on genes involved in human mental diseases.

Research Products

• [Journal Article] Evolutionary Pattern of Gene Homogenization between Primate-Specific Paralogs after Human and Macaque Speciation using the 4-2-4 method. (2010)
  • Author(s): Ezawa K., Ikeo K., Gojobori T., Saitou N.
  • Journal Title: Molecular Biology and Evolution (in press)
  • Peer Reviewed
• [Journal Article] MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. (2010)
  • Author(s): Kryukov K., Saitou N.
  • Journal Title: BMC Bioinformatics vol.11 Pages: 142
  • Peer Reviewed
• [Journal Article] Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis. (2009)
  • Author(s): Kitano T., Noda R., Takenaka O., Saitou N.
  • Journal Title: Molecular Phylogenetics and Evolution vol.51 Pages: 465-471
  • Peer Reviewed
• [Journal Article] Estimation of bacterial species phylogeny through oligonucleotide frequency distances (2009)
  • Author(s): Takahashi M., Krukov K., Saitou N.
  • Journal Title: Genomics vol.93 Pages: 525-533
  • Peer Reviewed
• [Journal Article] Skewed Matrilineal Genetic Composition in a Small Wild Chimpanzee Community. (2009)
  • Author(s): Shimada M.K., Hayakawa S., Fujita S., Sugiyama Y., Saitou N.
  • Journal Title: Folia Primatologica vol.80,no.1 Pages: 19-32
  • Peer Reviewed
• [Journal Article] Variable number of tandem repeat polymorphisms of DRD4: re-evaluation of selection hypothesis and analysis of association with schizophrenia. (2009)
  • Author(s): Hattori E., Nakajima M., Yamada K., Iwayama Y., Toyota T., Saitou N., Yoshikawa T.
  • Journal Title: European Journal of Human Genetics vol.17 Pages: 793-801
  • Peer Reviewed
• [Journal Article] Possible involvement of SINEs in mammalian-specific brain formation. (2008)
  • Author(s): Sasaki T., Nishihara H., Hirakawa M., Fujimura K., Tanaka M., Kokubo N., Kimura-Yoshida C., Matsuo I., Sumiyama K., Saitou N. Shimogori T., Okada N.
  • Journal Title: Proceedings of the National Academy of Sciences of U.S.A. vol.105,no.11 Pages: 4220-4225
  • Peer Reviewed
• [Journal Article] Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies. (2008)
  • Author(s): Liu Y. -H., Takahashi A., Kitano T., Koide T., Shiroishi T., Moriwaki K., Saitou N.
  • Journal Title: Genes and Genetic Systems vol.83 Pages: 77-88
  • Peer Reviewed
• [Journal Article] Biological implication for loss of function at major histocompatibility complex loci (2008)
  • Author(s): Sawai H., Go Y., Satta Y.
  • Journal Title: Immunogenetics vol.60no.6 Pages: 295-302
  • Peer Reviewed
• [Journal Article] Population genetic analysis of the N-acylsphingosine amidohydrolase gene associated with mental activity in humans. (2008)
  • Author(s): Kim H.L., Satta Y.
  • Journal Title: Genetics vol.178,no.3 Pages: 1505-1515
  • Peer Reviewed
• [Journal Article] On the origin and function of an insertion element VPaI-1 specific to post-1995 pandemic Vibrio parahaemolyticus strains. (2008)
  • Author(s): Nishioka T., Kamruzzaman M., Nishibuchi M., Satta Y.
  • Journal Title: Genes Genetic Syst Vol.83no.2 Pages: 101-110
  • Peer Reviewed
• [Journal Article] The origin and evolution of human ampliconic gene families and ampliconic. (2007)
  • Author(s): Bhomick, B.K., Satta, Y., Takahata, N.
  • Journal Title: Genome Res. vol.17 Pages: 441-450
  • Peer Reviewed
• [Journal Article] Genomewide search of gene conversions in duplicated genes of mouse and rat. (2006)
  • Author(s): Ezawa K., OOta S., Saitou N.
  • Journal Title: Molecular Biology and Evolution vol.23,no.5 Pages: 927-940
  • Peer Reviewed
• [Journal Article] Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. (2006)
  • Author(s): Kuroki Y., Toyoda A., Noguchi H., Taylor T.D., Itoh T., Kim D.S., Kim D.W., Choi S.H., Kim I.C., Choi H.H., Kim Y.S., Satta Y., Saitou N., Yamada T., Morishita S., Hattori M., Sakaki Y., Park H.S., Fujiyama A.
  • Journal Title: Nature Genetics vol.38,no.2 Pages: 158-167
  • Peer Reviewed
• [Journal Article] Origin and evolution of gene for prolactin-induced protein. (2006)
  • Author(s): Kitano T., Tian W., Umetsu K., Yuasa I., Yamazaki K., Saitou N., Osawa M.
  • Journal Title: Gene vol.383 Pages: 64-70
  • Peer Reviewed
• [Journal Article] Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals (2006)
  • Author(s): Kaneko S., Aki I., Tsuda K., Mekada K., Moriwaki K., Takahata N., Satta Y.
  • Journal Title: Genetics vol.172,no.4 Pages: 2421-2429
  • Peer Reviewed
• [Journal Article] he origin and evolution of human ampliconic gene families and ampliconic structure. (2006)
  • Author(s): Bhowmick B.K., Satta Y., Takahata N.
  • Journal Title: Genome Research vol.17,no.4 Pages: 441-450
  • Peer Reviewed
• [Journal Article] Evolutionary conservation of 5' upstream sequence of nine genes between human and great apes. (2005)
  • Author(s): Kitano T., Saitou N.
  • Journal Title: Genes and Genetic Systems vol.80,No.3 Pages: 225-232
  • Peer Reviewed
• [Presentation] Evolution of primate-specific highly conserved non-coding regions. (2010)
  • Author(s): Saitou N.
  • Organizer: An International Conference on Mathematics, Evolution, and Development. CAS-MPG Partner Institute for Computational Biology
  • Place of Presentation: Shanghai, China.
  • Year and Date: 2010-03-22
• [Presentation] MISHIMA - a new method for rapid construction of multiple alignments for large number of sequences up to bacterial genome size. (2010)
  • Author(s): Saitou N.
  • Organizer: Japan-Korea-China Bioinformatics Symposium.
  • Place of Presentation: ANA Intercontinental Hotel Tokyo, Tokyo
  • Year and Date: 2010-03-01
• [Presentation] 自然淘汰論から中立進化論へ (2009)
  • Author(s): 斎藤成也
  • Organizer: 日本人類学会公開講演会「ダーウィンと人類進化」
  • Place of Presentation: 東京大学
  • Year and Date: 2009-11-03
• [Presentation] Evolutionary patterns of gene homogenization between primate-specific paralogs after human and macaque speciation. (2009)
  • Author(s): Saitou N.
  • Organizer: PICB Workshop on Cpmparative Sequence Analysis 2009. CAS-MPG Partner Institute for Computational Biology
  • Place of Presentation: Shanghai, China.
  • Year and Date: 2009-10-22
• [Presentation] MISHIMA - Method for Inferring Sequence History In terms of Multiple Alignment. (2009)
  • Author(s): Saitou N.
  • Organizer: PICB Minisymposium on Current Challenges in Computational Biology.
  • Place of Presentation: CAS-MPG Partner Institute for Computational Biology, Shanghai, China.
  • Year and Date: 2009-09-12
• [Presentation] Evolutionary Pattern of Gene Homogenization between Primate-Specific Paralogs after Human and Macaque Speciation. (2009)
  • Author(s): Saitou N., Ezawa K., Ikeo K., Gojobori T.
  • Organizer: SMBE Annual Meeting 2009
  • Place of Presentation: Iowa City, USA
  • Year and Date: 2009-06-05
• [Presentation] Evolution of vertebrate-specific, primate-specific and mammalian-specific highly conserved non-coding genomic region. (2009)
  • Author(s): Saitou N.
  • Organizer: Japan-Germany Colloquium 2009 "Evolutionary Genomics"
  • Place of Presentation: Bonn, Germany.
  • Year and Date: 2009-03-10
• [Presentation] Evolution of protein non-coding DNA region in vertebrates. (2009)
  • Author(s): Saitou N.
  • Organizer: Japan-Korea-China Bioinformatics Symposium
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 2009-02-28
• [Presentation] Molecular Evolutionary and Population Genetics of Human Mental Related Genes. Symposium『Darwinian selection identified from comparative genomics』 (2008)
  • Author(s): 颯田葉子
  • Organizer: 第31回日本分子生物学会年会、第81回日本生化学会大会
  • Place of Presentation: 神戸ポートピアホテル, 神戸
  • Year and Date: 2008-12-10
• [Presentation] 哺乳類および霊長類に特有な高度に保存されている塩基配列の進化 (2008)
  • Author(s): 斎藤成也
  • Organizer: 日本分子生物学会・日本生化学合同大会
  • Place of Presentation: 神戸ポートピアホテル, 神戸
  • Year and Date: 2008-12-09
• [Presentation] 新しいアルゴリズムに基づく大規模塩基配列を高速に多重整列するシステム (2008)
  • Author(s): 斎藤成也. MISHIMA
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋大学, 名古屋市
  • Year and Date: 2008-09-04
• [Presentation] Welcome to world of phylogenetic networks! Symposium S3: Phylogenetic Networks for Evolutionary Studies. (2008)
  • Author(s): Saitou N.
  • Organizer: SESJ annual meeting
  • Place of Presentation: University of Tokyo, Komaba Campus, Tokyo.
  • Year and Date: 2008-08-22
• [Presentation] Utility of phylogenetic network for deciphering nucleotide sequence history. (2008)
  • Author(s): Saitou N.
  • Organizer: NIG International Symposium. National Institute of Informatics
  • Place of Presentation: Tokyo.
  • Year and Date: 2008-03-28
• [Presentation] 遺伝子変換による重複遺伝子の均質化 (2007)
  • Author(s): 斎藤成也
  • Organizer: 日本分子生物学会・日本生化学合同大会シンポジウム
  • Place of Presentation: パシフィコ横浜、横浜市
  • Year and Date: 2007-12-14
• [Presentation] Evolutionary analysis on primates. (2007)
  • Author(s): Saitou N.
  • Organizer: 79th Annual Meeting of the Genetics Society of Japan
  • Place of Presentation: 9. 21. 2007. Okayama, Japan
  • Year and Date: 2007-09-21
• [Presentation] Evolution of ultra-conserved elements in mammals (2007)
  • Author(s): Saitou N.
  • Organizer: SMBE Annual Meeting 2007
  • Place of Presentation: Hallifax, Canada.
  • Year and Date: 2007-06-27
• [Presentation] Neccessity of Non-Tree Structure in Nuclear DNA Phylogeny. (2007)
  • Author(s): Saitou N.
  • Organizer: A tree of life constructed by genome-wide information
  • Place of Presentation: Tibet, China
  • Year and Date: 2007-06-08
• [Presentation] Relic of ancient recombinations in gibbon ABO blood group genes suggests transspecific polymorphism. (2006)
  • Author(s): Saitou N.
  • Organizer: GlycoT2006
  • Place of Presentation: Tsukuba, Japan.
  • Year and Date: 2006-06-28
• [Presentation] 霊長類ゲノムにひそむ網状の系統関係 (2006)
  • Author(s): 斎藤成也
  • Organizer: 特定領域研究「ゲノム」4領域一般公開講演会
  • Place of Presentation: 朝日ホール、東京
  • Year and Date: 2006-01-29
• [Presentation] What kind of information can we extract from evolutionary genome sequence analysis? (2005)
  • Author(s): Saitou N.
  • Organizer: KOGO meeting, Symposium 10, Comparative Genomics.
  • Place of Presentation: Seoul, Korea.
  • Year and Date: 2005-09-09
• [Presentation] 哺乳類ゲノムの比較解析～系統樹では表現できない進化関係の探索～. シンポジウム『ゲノム比較から見えてきたゲノムと生命の進化の全貌』 (2005)
  • Author(s): 斎藤成也
  • Organizer: 日本進化学会大会
  • Place of Presentation: 東北大学, 仙台
  • Year and Date: 2005-08-27
• [Book] 自然淘汰論から中立進化論へ～進化学のパラダイム転換～ (2009)
  • Author(s): 斎藤成也
  • Total Pages: 228
  • Publisher: ntt出版
• [Book] 絵でわかる人類の進化 (2009)
  • Author(s): 斎藤成也
  • Total Pages: 192
  • Publisher: 講談社サイエンティフィック
• [Book] 環境を<感じる>生物センサーの進化 (2009)
  • Author(s): 郷康広・颯田葉子
  • Total Pages: 114
  • Publisher: 岩波書店
• [Book] ゲノム進化学入門 (2007)
  • Author(s): 斎藤成也
  • Total Pages: 257
  • Publisher: 共立出版
• [Book] ゲノム進化を考える (2007)
  • Author(s): 斎藤成也
  • Total Pages: 120
  • Publisher: サイエンス社
• [Book] ゲノムはここまで解明された (2007)
  • Author(s): 斎藤成也
  • Total Pages: 179
  • Publisher: ウェッジ
• [Book] 霊長類ゲノムにひそむ網状の系統関係. 『ゲノムは何をどのように決めているのか』 (2007)
  • Author(s): 斎藤成也
  • Total Pages: 198-1208
  • Publisher: クバプロ
• [Book] 脊椎動物の比較ゲノム:遺伝子間領域の比較解析. 細胞工学別冊『比較ゲノム学から読み解く生命システム』 (2007)
  • Author(s): 隅山健太・斎藤成也
  • Total Pages: 50-53
  • Publisher: 秀潤社
• [Book] 遺伝子からみたヒトの進化, シリーズ進化学第5巻『ヒトの進化』 (2006)
  • Author(s): 颯田葉子・斎藤成也
  • Total Pages: 65-108
  • Publisher: 岩波書店
• [Book] 類人猿と人類はどれほど近いか. シリーズヒトの科学第1巻『ヒトはどのようにしてつくられたか』 (2006)
  • Author(s): 斎藤成也
  • Total Pages: 81-93
  • Publisher: 岩波書店
• [Remarks] データベース/ソフトウェアMISHIMA
  • URL: http://sayer.lab.nig.ac.jp/~saitou/MISHIMA.html
• [Remarks]
  • URL: http://sayer.lab.nig.ac.jp/index-j.html